AU2017380107A1 - Isolation of a novel pestivirus causing congenital tremor A - Google Patents

Abstract

The present invention relates to a new pestivirus useful in the fields of veterinary virology and vaccines. Specifically, it relates to an isolated polynucleotide originating from pestivirus and a pestivirus, to vaccines and medical uses thereof, to chimeric virus comprising the polynucleotide and to expression vectors for heterologous expression of polypeptides.

Description

ISOLATION OF A NOVEL PESTIVIRUS CAUSING CONGENITAL TREMOR A

FIELD OF THE INVENTION

The present invention relates to a new pestivirus useful in the fields of veterinary virology and vaccines. Specifically, it relates to an isolated polynucleotide originating from pestivirus, to vaccines and medical uses thereof, to chimeric virus comprising the polynucleotide and to the use of said virus as viral vector for expression of heterologous polypeptides.

BACKGROUND OF THE INVENTION

Pestiviruses are single-stranded, positive-sense RNA viruses. The pestiviral genome has a length of about 11.5 to 12.5 kb and contains one large open reading frame, which is flanked by non-translated regions (NTR) at the 5' and 3' genome ends. The resulting large polyprotein is co- and post-translationally processed into 12 mature viral proteins: an autoprotease (Npro), capsid protein (C), three envelope proteins (Erns, E1, E2) and the non-structural proteins (p7, NS2, NS3, NS4A, NS4B, NS5A, NS5B) which are conserved among pestiviruses regarding genome localization and catalytic residues.

The genus pestivirus is classified within the family Flaviviridae and consists of four species approved by the International Committee on Taxonomy of Viruses. The classification of pestiviruses is based on nucleotide sequence, host range and serological differences. The 5' NTR is the region most frequently used for the phylogenetic analysis of pestiviruses but more variable genes (Npro or E2) have also been employed. Nevertheless, a comparison of full genome sequences enables the most precise phylogenetic typing. Besides Bovine viral diarrhea virus-1 (BVDV-1) and BVDV-2, Border disease virus (BDV) and Classical swine fever virus (CSFV), several unassigned strains and/or tentative species are represented by the so called atypical pestivirus strains. Atypical pestiviruses have been isolated from exotic species within the order Artiodactyla, especially bovine, ovine and porcine hosts. Recent studies detected pestiviral sequences in rats and bats suggesting a broader host range of pestiviruses. However, until now all isolated pestiviruses originate from ungulates.

One of the most dangerous viral epidemics in swine, CSFV, has been eradicated from the domesticated swine population in most developed countries since decades. Infections of swine with other pestivirus species have been detected, for

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-2example the introduction of certain BDV and BVDV strains pointing at the capacity of adaptation. An “atypical” porcine pestivirus was identified in 2003 in a commercial pig breeding farm in Australia, later termed Bungowannah virus. This well studied virus caused reproductive disorders, stillbirth and sudden death in piglets due to myocarditis. The marked sequence diversity of this virus resulted in the failure of its detection by the established pan-pestivirus diagnostic methods (ELISA, crossneutralization tests, RT-PCRs). The documented pathogenicity of Bungowannah virus alarmed the pork-producing industry because of the potential economic impact. The loss of about 50,000 animals was only reported from two affected farms in Australia. Bungowannah virus is still present in one farm but this virus or relatives were never found at other locations.

A novel group of closely related porcine pestiviruses has been discovered recently forming the tentative species of “atypical porcine pestiviruses (APPV)”. These viruses were first identified in North America and subsequently also found in Germany, the Netherlands and Austria (Schwarz et al., 2017. Congenital infection with atypical porcine pestivirus (APPV) is associated with disease and viral persistence. Veterinary Research 48:1). There is strong evidence that APPVs are representing the infectious agents behind the type A-ll congenital tremor (CT) syndrome of piglets. A-ll CT is prevalent worldwide and a common syndrome in newborn piglets. APPV is very difficult to propagate in vitro and hence Koch’s postulates have only partly been fulfilled. Nevertheless, transmission of the agent from affected piglets to pregnant sows reproduced the clinical signs. The clinical features are characterized by a generalized mild to severe shaking of the whole body that pathohistologically is associated with variable hypomyelination of brain and spinal cord. Hypomyelination is a characteristic lesion apparent in the brain of sheep, cattle and pigs after late gestation state in utero infection with BDV, BVDV and CSFV yielding newborn “hairy shaker” lambs, shaking calves and A-l CT affected piglets. Infections with most if not all pestiviruses during gestation may have a detrimental effect on the embryo or fetus, causing stillbirth, malformations or neurological defects.

In view of the importance of an effective and safe as well as detectable prophylaxis and treatment of pestiviral infections, there is still a strong and unmet need for an immunogenic pestivirus, with good viral replication and high potential for induction of immunity.

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-3SHORT DESCRIPTION OF THE INVENTION

The object is met by the subject matter of the invention as claimed.

The novel isolated pestivirus has low pathogenicity in animals and can lead to fast and reliable sero-conversion even after natural infection routes. Therefore the virus is highly applicable for vaccination purposes.

The inventors have named the novel pestivirus Linda virus.

According to the invention there is provided an isolated polynucleotide comprising a nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 2 or a sequence with at least 60%, specifically at least 70% identity thereto.

Specifically, said polynucleotide is an infectious polynucleotide.

In an embodiment of the invention, the polynucleotide is present in a cell, specifically in a host cell.

According to the invention there is also provided an RNA polymerase promoter operably linked to the polynucleotide.

According to a further embodiment, the polynucleotide further comprises an exogenous, heterologous polynucleotide.

According to an embodiment, the polynucleotide is present in a vector.

In a further embodiment there is provided a cDNA polynucleotide of SEQ ID NO: 1.

In a further embodiment there is provided a cDNA polynucleotide having at least 60%, at least 65%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, at least 99.5% identity to SEQ ID NO: 1.

In a further embodiment there is provided a polynucleotide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, 99.5% identity to SEQ ID NO: 1 or SEQ ID NO: 2.

Provided herein is also a polynucleotide comprising a sequence selected from the group of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29 or any combinations thereof or a sequence with at least 90%, specifically at least 95% identity thereto or any combinations thereof.

It is highly advantageous that the pestivirus of the invention is clearly distinct from other viruses such as Bungowannah or APPV. The pestivirus of the invention may easily be propagated on host cells such as SK-6 or PK-15 cells to high titers, such as a titer of >10⁷TCID₅₀, without the need for adaptation.

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-4Provided herein is also a composition comprising a porcine pestivirus having a nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 2 or a sequence having at least 60%, specifically at least 70%, 75%, 80%, 85%, 90%, 95%, 99% identity to SEQ ID NO: 1 or SEQ ID NO: 2. According to a specific embodiment, the at least 60%, specifically at least 70%, 75%, 80%, 85%, 90%, 95%, 99% identity to SEQ ID NO: 1 or SEQ ID NO: 2 is given over the entire length of the sequences.

According to the invention there is also provided a composition comprising a porcine pestivirus comprising an amino acid sequence of SEQ ID NO: 3 or a sequence with at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, 99.5% identity to SEQ ID NO: 3. According to a specific embodiment, the at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, 99.5% identity to SEQ ID NO: 3 is given over the entire length of the sequence.

According to the invention there is also provided a composition comprising a porcine pestivirus having an amino acid sequence selected from SEQ ID NO: 4 (Npro), SEQ ID NO: 5 (Core), SEQ ID NO: 6 (Erns), SEQ ID NO: 7 (E1), SEQ ID NO: 8 (E2), SEQ ID NO: 9 (P7), SEQ ID NO: 10 (NS2), SEQ ID NO: 11 (NS3), SEQ ID NO: 12 (NS4A), SEQ ID NO: 13 (NS4B), SEQ ID NO: 14 (NS5A), SEQ ID NO: 15 (NS5B), or any combinations thereof.

Specifically, the composition comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 sequences of SEQ ID NO: 4 (Npro), SEQ ID NO: 5 (Core), SEQ ID NO: 6 (Erns), SEQ ID NO: 7 (E1), SEQ ID NO: 8 (E2), SEQ ID NO: 9 (P7), SEQ ID NO: 10 (NS2), SEQ ID NO: 11 (NS3), SEQ ID NO: 12 (NS4A), SEQ ID NO: 13 (NS4B), SEQ ID NO: 14 (NS5A), SEQ ID NO: 15 (NS5B).

According to a further embodiment of the invention, there is provided a composition wherein the porcine pestivirus is inactivated or attenuated, specifically there is provided a chemically inactivated virus which is inactivated by treatment with an inactivating agent selected from the group consisting of binary ethyleneimine, ethyleneimine, acetylethyleneimine, beta-ethyleneimine, beta-propiolactone, glutaraldehyde, ozone, and formaldehyde.

There is also provided a composition containing a pestivirus of the invention, wherein the pestivirus is a physically inactivated pestivirus, specifically inactivated by treatment with UV radiation, X-ray radiation, gamma-radiation, freeze-thawing, and/or heating.

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-5According to an alternative embodiment of the invention, the pestivirus is attenuated by modifying the Npro, Erns or N2-3 gene.

According to a specific embodiment, the pestivirus is in freeze-dried form.

For administration, the composition comprises a titer of at least about 10⁴, specifically at least 10⁵, 10⁶, 10⁷, 10⁸ TCID₅₀ per dose.

According to a further embodiment of the invention, there is also provided a pharmaceutical composition comprising a polynucleotide, a composition, a vector or a chimeric pestivirus as described herein.

The present invention also provided a porcine pestivirus vector comprising a nucleotide sequence of SEQ ID NO: 1 or a sequence having at least 60%, specifically at least 70%, 75%, 80%, 85%, 90%, 95%, 99% identity to SEQ ID NO: 1 and a sequence encoding a heterologous sequence.

The present invention also provided a porcine pestivirus vector comprising a nucleotide sequence of SEQ ID NO: 2 or a sequence having at least 60%, specifically at least 70%, 75%, 80%, 85%, 90%, 95%, 99% identity to SEQ ID NO: 2 and a sequence encoding a heterologous sequence. Said heterologous sequences can be any regulatory sequence or sequence encoding selection markers. Specifically, a heterologous sequence is selected from one or more viruses consisting of the group of bovine viral diarrhea virus-1 (BVDV-1) and BVDV-2, border disease virus (BDV), classical swine fever virus (CSFV), atypical pestivirus (APPV), specifically NRPV, PEDV, RaPV, border disease virus, isolates from reindeer, giraffe, HoBi pestivirus and Bungowannah virus.

Specifically, said heterologous sequence encodes a surface antigen from said viruses. More specifically, the heterologous sequence encodes a surface antigen selected from the group of sequences comprising SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47 and SEQ ID NO: 48 or any combination or fragment or part thereof.

According to an alternative embodiment, said heterologous sequence encodes a surface antigen from any virus of interest such as, but not limited to PEDV, African swine fever porcine circovirus and PRRSV.

Specifically, the heterologous sequence is inserted within the 5'or 3' terminal region or at the 5'or 3'terminus of Npro or E2.

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-6According to an alternative embodiment, the heterologous sequence encodes a fusion peptide with Npro, E2 or E1 protein of the pestivirus.

The invention also provides a chimeric pestivirus comprising a nucleotide sequence of SEQ ID NO: 1or SEQ ID NO: 2 or a sequence having at least 60%, specifically at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% identity to SEQ ID NO: 1or SEQ ID NO: 2, and a foreign polypeptide.

According to the invention there is provided a vaccine for animals comprising a polynucleotide, a composition, a vector, ora chimeric pestivirus as described herein.

Further provided herein is a kit for inducing an immune response against porcine pestivirus infection in an animal, specifically in a pig, said kit comprising a composition or vaccine as described herein and instructions for administering said composition to said animal.

Further provided herein is a method for protecting an animal, specifically a pig, specifically a piglet, against a disease associated with pestivirus, wherein the method comprises administering to a pregnant sow, a boar, a post weaner or a gilt, or to a sow or gilt prior to breeding, the composition or vaccine as described herein, in an amount sufficient to protect the animal, specifically for protecting or treating the animal against congenital tremor, specifically congenital tremor A-ll.

According to a specific embodiment of the invention, the composition is parenterally administered, specifically intramuscularly, subcutaneously, intradermally, or intravenously using a needle and syringe, or a needleless injection device; and mucosal administration nasally or orally.

According to an embodiment of the invention, a method for detecting pestivirus is provided, wherein a sample is tested with RT PCR using at least one of the primers selected from 5’-GTKATHCAATACCCTGARGC-3’ (SEQ ID NO: 32) and 5’GGRTTCCAGGARTACATCA-3’ (SEQ ID NO: 33).

Further provided herein is a diagnostic assay for detecting pestivirus, comprising at least one of the primers selected from SEQ ID NO: 32 and SEQ ID NO: 33.

Also provided herein is a diagnostic kit for detecting pestivirus, comprising at least one of the primers selected from SEQ ID NO: 32 and SEQ ID NO: 33, further comprising devices and instructions.

According to a further embodiment also a method for detecting pestivirus antigen having an amino acid sequence of SEQ ID NO: 3 or an amino acid sequence

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-7of at least 60% identity in a biological sample is provided, said method comprising contacting a biological sample, specifically blood, organ or excretion samples, with an antibody specifically binding to an antigen of said pestivirus if present in said sample; and detecting said antibody binding to said antigen in said sample.

According to a specific embodiment, the antibody is a monoclonal antibody, specifically it is monoclonal antibody 6A5 as described by Gilmartin A.A. et al., 2012, Protein Eng Des Sei 25.

According to the invention there is also provided a method for preparing the inventive vaccine comprising the sequential steps of

a) infecting a host cell culture with a polynucleotide, a vector, or a chimeric pestivirus as described herein,

b) incubating said host cell culture for virus propagation,

c) harvesting the host cell culture, and optionally

d) isolating the virus from the culture and

e) admixing to the culture with a pharmaceutically acceptable carrier.

The embodiment of the invention also provides the use of a polynucleotide, a vector, a composition, or a chimeric pestivirus as described herein, for preparing a vaccine for animals.

Further provided herein is a polynucleotide, a vector, a composition, or a chimeric pestivirus as described herein or any combinations thereof, for use in a vaccine or for the treatment of animals.

Also provided herein is a method for controlling an infection with a pestivirus in animals, wherein the vaccine as described herein is combined with a diagnostic kit or assay as described herein.

FIGURES

Figure 1: Histopathological examination in piglets with congenital tremor (CT).

Figure 2: Phylogenetic genome analysis of Linda virus, atypical pestivirus strains and the pestiviral type strains.

Figure 3: Phylogenetic analysis of pestiviral polyproteins.

Figure 4: Amino acid comparison of Linda virus E2 protein. E2 sequences of Linda virus (SEQ ID NO: 8) Bungowannah virus (SEQ ID NO: 36), Pronghorn (SEQ ID NO: 37), Giraffe (SEQ ID NO: 38), BDV (SEQ ID NO: 39), Reindeer (SEQ ID NO: 40), Sheep (SEQ ID NO: 41), CSFV (SEQ ID NO: 42), BVDV-1 (SEQ ID NO: 43), BVDV-2 (SEQ ID NO:

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-844), BVDV-3 (SEQ ID NO: 45), Rat E2 (SEQ ID NO: 46), Bat E2 (SEQ ID NO: 47), APPV E2 (SEQ ID NO: 48)

Figure 5: Propagation of Linda pestivirus in cell culture.

Figure 6: Validation of a cross-reactive monoclonal antibody

Figure 7: Full length DNA sequence of Linda virus (SEQ ID NO: 1).

Figure 8: Full length RNA sequence of Linda virus (SEQ ID NO: 2).

Figure 9: Amino acid sequence of Linda virus (SEQ ID NO: 3), amino acids in bold letters mark possible insertion sites. Npro sequence is in italic letters.

Figure 10: Amino acid sequences of Linda virus a) Npro (SEQ ID NO: 4), b) Core (SEQ ID NO: 5), c) Erns (SEQ ID NO: 6), d) E1 (SEQ ID NO: 7), e) E2 (SEQ ID NO: 8), f) P7 (SEQ ID NO: 9), g) NS2 (SEQ ID NO: 10), h) NS3 (SEQ ID NO: 11), i) NS4A (SEQ ID NO: 12), j) NS4B (SEQ ID NO: 13), k) NS5A (SEQ ID NO: 14), I) NS5B (SEQ ID NO: 15).

Figure 11: DNA sequences of Linda virus proteins and untranslated regions, a) 5’-UTR (SEQ ID 16), Npro (SEQ ID 17), c) Core (SEQ ID 18), d) Erns (SEQ ID 19), e) E1 (SEQ ID 20), f) E2 (SEQ ID 21), g) P7 (SEQ ID 22), h) NS2 (SEQ ID 23), i) NS3 (SEQ ID 24), j) NS4A (SEQ ID 25), k) NS4B (SEQ ID 26), I) NS5A (SEQ ID 27), m) NS5B (SEQ ID 28), n) 3'- UTR (SEQ ID 29).

DETAILED DESCRIPTION

Specific terms as used throughout the specification have the following meaning.

The terms “comprise”, “contain”, “have” and “include” as used herein can be used synonymously and shall be understood as an open definition, allowing further members or parts or elements. “Consisting” is considered as a closest definition without further elements of the consisting definition feature. Thus “comprising” is broader and contains the “consisting” definition.

The term “about” as used herein refers to the same value or a value differing by +/-5% of the given value.

In the sequence identifiers presented herewith, nucleotides are represented in standard IUPAC-IUB code of DNA. However, as the skilled person will understand, the pestivirus genomic sequences in nature are in RNA form, where a T will be a U. The pestivirus RNA sequence of the invention specifically is SEQ ID NO: 2.

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-9The term “infectious” refers to a polynucleotide having the sequence of SEQ ID NO. 2 or at least parts or fragments thereof such as the NSP encoding region that can be fully replicated in a host cell or an animal.

The terms “homology” or “identity” can be used interchangeably and refer to the identity of the respective nucleic acid residues. The percentage of identical residues (percent identity) is used to quantify the homology/identity.

The term “attenuated” as used herein refers to a virus having a polynucleotide sequence derived from or originating from pestivirus having a nucleotide sequence of SEQ ID No. 1 or SEQ ID NO. 2 or at least parts or fragments thereof, wherein the virus has a reduced virulence as compared to another virus of the same species or isolate, such as a wild type virus or isolate. In fact, attenuated means to display a reduced dissemination through the body of an infected target animal, e.g. fetal infection; to induce less pathology such as (signs of) disease; and/or to display a reduced spread into the environment. Whether the pestivirus is attenuated, and whether that level of attenuation is sufficient for use according to the invention, e.g. regarding its use in a live vaccine, can be determined using standard procedures either in vitro or in vivo. For example, by comparing viruses, comparing the effect of a modification on the viral replication rate in cell culture, or in an infected animal by checking viral presence in different tissues or organs or in the feces of said animal, and monitoring clinical, macroscopic, or microscopic signs of disease in an animal or a fetus.

Attenuation can be established but is not limited by modifying the Npro gene or the NS2-3 gene of the inventive virus, whereby the pestivirus has a modification, especially a mutation of an epitope located in the Npro protein, the NS2 protein, or a duplication of certain genome regions so that the NS2-3 cleavage is enhanced. This is not affected by mutations of an epitope located in a helicase domain of the NS3 protein, so that the epitope is not or less reactive with an antibody against that epitope compared to a wild-type pestivirus.

The term “inactivated” as used herein refers to a virus having a polynucleotide sequence derived from or originating from pestivirus having a nucleotide sequence of SEQ ID No. 1 or SEQ ID NO. 2 or at least parts or fragments thereof, wherein the virus has lost its virulence as compared to another virus of the same species or isolate, such as a wild type virus or isolate by killing the virus with chemicals, heat, or radiation.

Inactivation can be established by, but is not limited to, the methods such as treatment with an inactivating agent selected from the group consisting of binary

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-10ethyleneimine, ethyleneimine, acetylethyleneimine, beta-ethyleneimine, betapropiolactone, glutaraldehyde, ozone, and formaldehyde.

As an alternative, physical inactivation can be performed such as but not limited to treatment with UV radiation, X-ray radiation, gamma-radiation, freeze-thawing, and/or heating.

A polynucleotide molecule is a biopolymer composed of 13 or more nucleotide monomers covalently bonded in a chain. DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are examples of the polynucleotides. As used herein, the term “exogenous polynucleotide” or “heterologous polynucleotide” refers to any polynucleotide sequence not naturally occurring in the pestivirus encoded by the sequences of the invention.

As used in this application, the term “amino acid” means one of the naturally occurring amino carboxylic acids of which proteins are comprised. The term “polypeptide” as described herein refers to a polymer of amino acid residues joined by peptide bonds, whether produced naturally or synthetically. Polypeptides of less than about 10 amino acids residues are commonly referred to as “peptides”.

A “protein” is a macromolecule comprising one or more polypeptide chains. A protein may also comprise non-peptidic components, such as carbohydrate groups. Carbohydrates and other non-peptidic substituents may be added to a protein by the cell in which the protein is produced, and will vary with the type of cell. Proteins are defined herein in terms of their amino acid backbone structures; substituents such as carbohydrate groups are generally not specified, but may be present nonetheless.

A polypeptide or amino acid sequence “derived from” a designated nucleic acid sequence refers to a polypeptide having an amino acid sequence identical to that of a polypeptide encoded in the sequence, or a portion thereof wherein the portion consists of at least 15 amino acids, specifically at least 20 amino acids, more specifically at least 30 amino acids, more specifically at least 50 amino acids, or which is immunologically identifiable with a polypeptide encoded in the sequence. This terminology also includes a polypeptide expressed from a designated nucleic acid sequence.

Specifically, the heterologous polypeptide is an immunogenic polypeptide.

In general, an immune response is generated to an antigen through the interaction of the antigen with the cells of the immune system. Immune responses may be broadly categorized into two categories: humoral and cell mediated immune

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-11responses (e.g., traditionally characterized by antibody and cellular effector mechanisms of protection, respectively). These categories of response have been termed Th1-type response (cell-mediated response), and Th2-type immune response (humoral response). Stimulation of an immune response can result from a direct or indirect response of a cell or component of the immune system to exposure to an immunogen. Immune responses can be measured in many ways including activation, proliferation or differentiation of cells of the immune system (e.g., B cells, T cells, dendritic cells, APCs, macrophages, NK cells, NKT cells, etc.); up-regulated or downregulated expression of markers and cytokines; stimulation of IgA, IgM, or IgG titer; splenomegaly (including increased spleen cellularity); hyperplasia and mixed cellular infiltrates in various organs. Other responses, cells, and components of the immune system that can be assessed with respect to immune stimulation are known in the art.

An “RNA polymerase promoter” according to the invention can be any region containing a sequence specifically recognized by an RNA polymerase (RNAP). The promoter can be operably linked to a sequence encoding a target RNA. One feature of present embodiments is the use of an RNA polymerase promoter and RNA polymerase such as any RNA polymerase and promoter known in the art. Certain examples herein, while not intended to be limiting, are T7 RNAP and T7 RNAP promoter. Other examples of polymerases with promoters include T7 RNAP with T7 Class III RNAP promoter or T7 phi 2.5 RNAP promoter, SP6 RNAP with SP6 RNAP promoter, T3 RNAP with T3 RNAP promoter, Syn5 RNAP with Syn5 RNAP promoter, E. coli RNAP with T5 promoter.

The term vector or plasmid vector as used herein defines a system comprising at least one vector suitable for transformation, transfection or transduction of a host cell. A vector per se thus denotes a cargo for the delivery of a biomolecule into a host cell of interest, wherein the biomolecule includes a nucleic acid molecule, including DNA, RNA and cDNA, or, in the case of a transfection system as vector, an amino acid molecule, or a combination thereof. The pestivirus of the invention can be used as vector according to the invention as it contains all regulatory elements necessary for replication. An alternative vector according to the present invention is a plasmid or expression vector that can be circular or linear. An expression vector can comprise one vector encoding at least one target molecule, preferably a nucleic acid molecule, to be introduced into a host cell. A vector of the vector system can also comprise more than one target molecules to be introduced. Alternatively, the vector system can be

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-12built from several individual vectors carrying at least one target molecule to be introduced. An expression vector additionally comprises all elements necessary for driving transcription and/or translation of a sequence of interest in a host cell, the expression vector is designed for. These elements comprise, inter alia, regulatory elements, which are involved in the regulation of transcription, including promoters and the like functional in the host cell of interest. Furthermore, an expression vector comprises an origin of replication and optionally depending on the type of vector and the intended use a selectable marker gene, a multiple cloning site, a tag to be attached to a sequence of interest, a chromosomal integration cassette and the like. The choice and possible modification of a suitable expression vector for use with a respective host cell and sequence of interest to be inserted into the expression vector is well within the capabilities of the person skilled in the art.

The term cDNA stands for a complementary DNA and refers to a nucleic acid sequence/molecule obtained by reverse transcription from an RNA molecule. As it is a standard method for the person skilled in the art to obtain cDNAs from a given sequence and to further use this cDNA or to clone said cDNA into a vector, preferably a plasmid vector, of interest.

As used herein, the term “operably linked” is used to describe the connection between regulatory elements and a gene or its coding region. Typically, gene expression is placed under the control of one or more regulatory elements, for example, without limitation, constitutive or inducible promoters, tissue-specific regulatory elements, and enhancers. A gene or coding region is said to be “operably linked to” or “operatively linked to” or “operably associated with” the regulatory elements, meaning that the gene or coding region is controlled or influenced by the regulatory element. For instance, a promoter is operably linked to a coding sequence if the promoter effects transcription or expression of the coding sequence.

The polynucleotide of the invention comprises a nucleotide sequence having at least 60%, specifically at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or 100% identity to SEQ ID NO: 1 or SEQ ID NO: 2.

In a certain embodiment, the polynucleotide consists of a nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

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-13Herein provided is further a composition comprising a porcine pestivirus having a nucleotide sequence with at least 60%, specifically at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or 100% identity to SEQ ID NO: 1 or SEQ ID NO: 2.

The polynucleotide sequences of the invention can be used for encoding pestivirus proteins or polypeptides, specifically Npro, Core, Erns, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B of the pestivirus of the invention.

Herein provided is a porcine pestivirus comprising a polyprotein having an amino acid sequence with at least 55% identity to SEQ ID NO: 3, specifically having at least 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%,

70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,

85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,

99.5%, 100% identity to SEQ ID NO: 3.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO:4 (Npro) or an amino acid sequence having at least 65%, specifically having at least 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 4.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 5 (Core protein) or an amino acid sequence having at least 85%, specifically having at least 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% sequence identity to SEQ ID NO: 5.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 6 (Erns protein) or an amino acid sequence having at least 75%, specifically having at least 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 6.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 7 (E1 protein) or an amino acid sequence having at least 75%, specifically having at least 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 7.

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-14Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 8 (E2) or an amino acid sequence having at least 55%, specifically having at least 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 8.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 9 (P7) or an amino acid sequence having at least 65%, specifically having at least 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 9.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 10 (NS2) or an amino acid sequence having at least 65%, specifically having at least 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 10.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 11 (NS3) or an amino acid sequence having at least 90%, specifically having at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 11.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 12 (NS4A) or an amino acid sequence having at least 85%, specifically having at least 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 12.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 13 (NS4B) or an amino acid sequence having at least 80%, specifically having at least 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 13.

Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 14 (NS5A) or an amino acid sequence having at least 55%, specifically having at least 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 14.

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-15Herein provided is also a polypeptide comprising an amino acid sequence of SEQ ID NO: 15 (NS5B) or an amino acid sequence having at least 75%, specifically having at least 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% to SEQ ID NO: 15.

As described herein, the pestivirus of the invention and the polynucleotide encoding said virus can be used for expressing one or more heterologous sequences.

Said heterologous sequence can be any sequence which is not originating or derived from the inventive pestivirus or from the polynucleotide of SEQ ID NO: 1 or SEQ ID NO: 2. Said heterologous sequence can encode a heterologous polypeptide or protein or part thereof from porcine circovirus 2 (PCV2), bovine viral diarrhea virus-1 (BVDV-1) and BVDV-2, border disease virus (BDV), classical swine fever virus (CSFV), atypical pestivirus (APPV), specifically NRPV, RaPV and border disease virus. The heterologous sequence can encode a surface antigen from any viruses or synthetic sequences derived therefrom as listed above. Specifically, the heterologous sequence is inserted at the 5'or 3'end of Npro or E2. More specifically, the heterologous sequence encodes a fusion peptide with Npro, E2 or E1 or a part or fragment of Npro, E2 or E1 of the pestivirus.

Even more specifically, the sequences can comprise any one of SEQ ID NO: 61 (Bungowannah), SEQ ID NO: 49 (pronghorn), SEQ ID NO: 50 (giraffe), SEQ ID NO: 51 (BDV), SEQ ID NO: 52 (reindeer), SEQ ID NO: 53 (sheep), SEQ ID NO: 54 (CSFV), SEQ ID NO: 55 (BVDV-1), SEQ ID NO: 56 (BVDV-2), SEQ ID NO: 57 (BVDV-3), SEQ ID NO: 58 (rat), SEQ ID NO: 59 (bat), SEQ ID NO: 60 (APPV) or any combination thereof or the part of the respective sequence encoding Npro, core, Erns, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A and NS5B protein of any of above listed pestivirus. Thus although full length amino acid sequence is given in any of SEQ ID Nos: 48 to SEQ ID NO: 60, the skilled person can easily determine the respective partial sequence of the protein of interest. Within the scope of the invention there is thus also a heterologous protein or polypeptide encoded by the virus of the invention having a sequence of Npro, core, Erns, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A and NS5B protein of SEQ ID Nos: 48 to 60, or a sequence having at least 90%, specifically at least 95, more specifically at least 99% identity therewith.

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-16The heterologous sequence can be inserted into the polynucleotide of SEQ ID NO: 1 or SEQ ID NO: 2 of the invention. Insertion can be performed by any method known to the skilled person.

According to an embodiment, the heterologous polypeptide is inserted within the N-terminal or C-terminal region.

As referred herein, the term “region” in connection with the N-terminus specifically means that the polypeptide is inserted within the first 15, specifically 10, specifically 5 N-terminal amino acids. In connection with the C-terminus, the heterologous sequence is inserted within 15, specifically 10, specifically 5 of the Cterminal amino acids.

For the invention, the heterologous polypeptide can be inserted within the Nterminal sequence MEFK (SEQ ID NO: 30) of Npro or the C-terminal sequence SCSD (SEQ ID NO: 31) of NPro. The heterologous sequence can also be inserted between the N-terminal methionine and glutamic acid (ME) and/or between the C-terminal cysteine and serine (CS) of Npro.

To allow sufficient cleavage of the heterologous polypeptide, proliferation sequences are additionally inserted at the C-terminal region of the heterologous polypeptide, for example, but not limited to, ubiquitin or picornavirus 2A protein is additionally inserted.

Alternatively, the heterologous polypeptide can also be inserted within the Nterminal 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 amino acids of the E2 sequence, specifically between the N-terminal amino acids leucine and glutamic acid.

A gene is chimeric if it is an assembly of parts that were not originally connected. For example, an assembly of parts of the same gene from different virus isolates or species. A chimeric gene encodes a chimeric protein that is effectively a fusion protein.

The term “chimeric pestivirus” according to the invention refers to the pestivirus of the invention comprising one or more of SEQ ID NO: 16, SEQ ID NO: 17, SEQID

NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQID

NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQID

NO: 28, SEQ ID NO: 29 or any combinations thereof or a sequence with at least 90%, specifically at least 95%. At least 99% identity thereto or any combinations thereof any further comprising a nucleotide sequence from a foreign polypeptide. Said foreign polypeptide can be originating from a genetically different pestivirus. The foreign

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-17polypeptide can be, but is not limited to, from bovine viral diarrhea virus-1 (BVDV-1) and BVDV-2, border disease virus (BDV), classical swine fever virus (CSFV), atypical pestivirus (APPV), specifically NRPV, PEDV, RaPV, border disease virus, isolates from reindeer, giraffe, HoBi pestivirus and Bungowannah virus or any fragment or derivative thereof.

The pestivirus, composition, vector or chimeric virus as described herein can be used for preparing a pharmaceutical composition, specifically a vaccine.

A vaccine is an immunogenic composition that has an inherent medical effect. A vaccine comprises an immunologically active component, and a pharmaceutically acceptable carrier. The 'immunologically active component', is one or more antigenic molecule(s) that is recognized by the immune system of a target, i.e. the pestivirus according to the invention per se or a vector or chimeric pestivirus as described herein, and that induces a protective immunological response. A vaccine generally is efficacious in reducing the level or the extent of an infection, for example by reducing the viral load or shortening the duration of viral replication in a host animal. Also a vaccine generally is effective in reducing or ameliorating the symptoms of disease that may be caused by, or may be the result of, such viral infection or replication, or by the animal's response to that infection.

The effect of the vaccine according to the invention is the prevention or reduction in animals of an infection by a pestivirus and/or of signs of disease that are associated with such virus infection or replication, through the induction of an immunological response, such as the induction of virus-neutralizing antibodies, and/or the induction of a cellular immune response.

The vaccines, specifically live attenuated or inactivated vaccines can be prepared in freeze-dried form. Freeze drying methods are well known in the art. The freeze-dried form can be, but is not limited to a cake, or a lyosphere. For reconstitution, the vaccine can be resuspended in a physiologically acceptable diluent. The diluent may contain additional compounds, such as an adjuvant.

The animals for which the vaccine according to the invention is intended are animals that are susceptible to infection with a pestivirus. Mainly these will be mammalian (non-human) animals, and will be members of the order Artiodactyla. Preferred target animals for the vaccine according to the invention are ruminants and swine; especially piglets. The term piglets specifically refers to post weaners, more specifically early weaners, having an age of about 10 days to 3 weeks, having about 4

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-185 kg, or conventional weaners, of about 3 to 5 weeks, having about 5 to 10 kg. Post weaners, however, may also have an age of about 12 weeks.

The term “boar” refers to an uncastrated male pig.

The term “gilt” refers to a young female pig. As used herein, a gilt is a pig that has not yet been bred, whether only a few months old or approaching a year. A gilt is intact, or capable of breeding and producing young, and her reproductive organs are not surgically or chemically altered. The term “sow” refers to an adult female swine.

A vaccine according to the invention may be a live-, a live-attenuated, an inactivated-, or a subunit vaccine, or any combination thereof.

Alternatively, a vaccine according to the invention, or a part thereof, may be a subunit vaccine. This can be prepared either from live- or from inactivated virus, by applying one or more (additional) steps for the fractionation or isolation of one or more parts of the viral particle. This comprises for instance preparing an extract, fraction, homogenate, or sonicate, all well known in the art.

The vaccine of the invention can also be a live vaccine. For the invention the term 'live' refers to the pestivirus of the invention that is capable of replication.

A vaccine according to the invention may also comprise an adjuvant. This is particularly useful when the vaccine is an inactivated- or a subunit vaccine. However, also live vaccines can comprise an adjuvant, although that should be carefully selected not to reduce the viability of the vaccine virus, even upon prolonged storage.

An adjuvant is a well-known vaccine ingredient, which in general is a substance that stimulates the immune response of a target in a non-specific manner. Examples of adjuvants for inactivated/subunit vaccines are, but are not limited to Freund's Complete or Incomplete adjuvants, vitamin E, aluminium compositions such as aluminium-phosphate or aluminium-hydroxide, Polygen™, non-ionic block polymers and polyamines such as dextran sulphate, polyacrylic acid, Saponin. Furthermore, peptides such as muramyldipeptides, dimethylglycine, tuftsin, are often used as adjuvant, and oil-emulsions, using mineral oil or light mineral (paraffin) oil; or nonmineral oil such as squalene, squalane, or vegetable oils, e.g. ethyl-oleate. A vaccineemulsion can be in the form of a water-in-oil (w/o), oil-in-water (o/w), water-in-oil-inwater (w/o/w), or a double oil-emulsion (DOE), etc. Alternatively, and more suitable for use with a live vaccine, other immuno-stimulatory components may be added to the vaccine according to the invention, such as a cytokine or an immunostimulatory

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-19oligodeoxynucleotide. The immunostimulatory oligodeoxynucleotide is preferably an immunostimulatory non-methylated CpG-containing oligodeoxynucleotide (INO).

The vaccine can be formulated as an injectable liquid, such as: a suspension, solution, dispersion, or emulsion. Alternatively the vaccine can be formulated in a freeze-dried form. Commonly vaccines are prepared sterile. Proper formulation may depend on various factors, such as the route of administration chosen.

An animal, specifically a piglet can be protected by vaccination against any disease associated with pestivirus by administering to an animal, especially to a pregnant sow, a boar, a post weaner, a gilt, or to a sow or gilt prior to breeding, the composition described herein in an amount sufficient to protect the piglet.

The disease is any disease caused by pestivirus, specifically it is congenital tremor, more specifically congenital tremor A-ll, classical swine fever and bovine diarrhea.

For administration, the composition, e.g. the vaccine can comprise a virus titer of a TCID₅₀ of at least about 1x10⁴, specifically at least 1x10⁵, 1x10⁶, 1x10⁷, 1x10⁸. The determination of the dosage, i.e. the amount of virus which is administered may depend on the mode of administration. For example, when administering the virus by oral or intranasal route, a TCID50 of at least 1x10⁶ shall be administered per dose, when administering the virus via intramuscular route, a TCID50 of at least 1x10⁴ shall be administered per dose, however higher titers are also encompassed, such as a titer of 1x10⁵, 1x10⁶, 1x10⁷ or more. The respective dose can be determined by the skilled person.

The present invention further provides a novel pan-pestivirus RT-PCR assay for detection of APPV, BDV, CSFV, BVDV-1, BVDV-2, and Linda-Virus. Specifically detection of genomes is with regard to the presence of pestivirus specific genes (Npro and Erns) as well as sequence homology to other pestiviruses in conserved genomic regions (NS3 and NS5B). The overall nucleotide identity between the isolated pestivirus of the invention (Linda virus) and the closest related known pestivirus (Bungowannah virus) is below 68.0%.

As an alternative, an assay can be devised for specifically detecting the pestivirus according to the invention, as a positive marker, screening for effective vaccination. Such an assay would use antibodies against a protein expressed by the pestivirus according to the invention, or would use the pestivirus as detection antigen for antibodies.

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-20For the invention, antibodies are immunoglobulin proteins or parts thereof that can specifically bind to an epitope. For sero-diagnosis, antibodies will typically be of IgG or IgM type. The antibodies can be intact or partial antibodies, e.g. a single chain antibody, or a part of an immunoglobulin containing the antigen- binding region. They can be of a different form: a (synthetic) construct of such parts, provided the antibodyparts still contain an antigen-binding site. Well known sub-fragments of immunoglobulins are: Fab, Fv, scFv, dAb, or Fd fragments, Vh domains, or multimers of such fragments or domains. Also the antibodies can be labelled in one or more ways to facilitate or amplify detection.

Therefore, in an embodiment of the method, differentiating vaccinated and nonvaccinated or infected and non-infected animals is allowed, using either the primer described herein, antibody 6A5 or serum neutralization assays employing the Linda virus and susceptible cell cultures. The method for differentiating according to the invention can be performed using any suitable method of immune-diagnostic assays. Often such immune-diagnostic assays will have a step for amplifying the signal strength, and one or more steps for washing away unbound, unspecific or unwanted components. The detection of a positive signal can be done in a variety of ways such as optically by detecting a color change, a fluorescence, or a change in particle size, or alternatively by the detection of radioactively labelled antigens or antibodies in immune-complexes. Similarly, the physical form of the test can vary widely and can e.g. employ a microtitration plate, a membrane, a dipstick, a biosensor chip, a gel matrix, or a solution comprising (micro-) carrier particles such as latex, metal, or polystyrene, etc.

The choice for a particular set-up of such an immune-diagnostic assay is usually determined by the type of input sample, the desired test sensitivity (correctly identifying a positive sample), and test specificity (correctly discriminating between true positive and true negative samples). Such properties are dependent of the strength and timing of an immune response, or the presence of a micro-organism. Further the requirements for test-economy such as the applicability on a large scale and the costs may be decisive for selection of a particular format.

Well-known immuno-diagnostic tests are: radioimmuno-assays, immunediffusion, immunofluorescence, immune-precipitation, agglutination, haemolysis, neutralization, and enzyme-linked immuno-sorbent assay or ELISA. Especially for large scale testing, the automation of the liquid handling, and/or of the result reading

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-21and processing, may be a requirement. ELISA's are easily scalable, and can be very sensitive. A further advantage is the dynamic range of its results because samples can be tested in a dilution range. Results are expressed in arbitrary units of absorbance, typically between 0.1 and 2.5 optical density (OD) units, or as 'blocking %', depending on the test properties and the settings of the technical equipment used for the readout. Routinely appropriate positive and negative control samples are included, and mosttimes samples are tested in multifold. Standardization is obtained by including (a dilution range of) a defined reference sample, which also allows matching a certain score to pre-set values for determining positives or negatives, and allows correlation to a biological meaning, for example: an amount of antigen to potency, or an amount of antibody to a level of immune protection.

Many variants of an ELISA set-up are known, but typically these employ immobilizing an antigen or an antibody to a solid phase, e.g. to a well of a microtitration plate. When an antibody is immobilized the test is called a 'capture' or 'sandwich' ELISA. Next a test sample is added, allowing the ligand (e.g. an antigen or antibody to be detected) to bind. Then a detector (an antibody, antigen, or other binding component) is added which often is conjugated to a label, for instance to an enzyme that can induce a color reaction, which can be read spectrophotometrically. Other types of label could be using luminescence, fluorescence, or radioactivity. The use of a labelled detector is intended to provide amplification of signal strength to enhance test sensitivity, however, it may also introduce background signal, reducing the signal to noise ratio.

Methods for collection and preparation of samples are well known in the art. Such samples can be any type of biological sample in which sufficient amounts of the virus or of the antibody to be detected is present. Typically these samples can be: blood, serum, milk, semen, urine, feces, or a tissue sample such as an ear-puncture.

What constitutes an appropriate immuno-assay e.g. for the detection of nonvaccine pestivirus may depend on the particulars of the sample, the virus, or other parameters of the test to be performed.

A diagnostic kit is also provided to perform the diagnostic assay and relates to a kit of parts for performing the methods for differentiating, or the method for diagnosing, both according to the invention. The kit comprises one or more components for applying the methods, in particular all parts needed for performing an RT-PCR and primers selected from SEQ ID NO: 26 and SEQ ID NO: 27. Optionally

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-22instructions how to perform the method, and how to read and interpret the results are included in the kit.

As stated above, the pestivirus of the invention can be efficiently propagated in cell culture.

In the method according to the invention, and for the amplification of the pestivirus according to the invention, the virus is produced in suitable host cells. This may be by way of inoculation onto the host cells and amplification by natural replication.

The host cell can be a primary cell, such as prepared from an animal tissue. Suitable host cells for the replication of pestivirus are well known in the art, and are generally publicly available. Methods, media, and materials for preparing and culturing a host cell according to the invention, are well known in the art. Examples of suitable host cells are cell lines such as: bovine cell lines such as: MDBK (Madin Darby bovine kidney); swine cell lines such as: PK15 or SK-6 (porcine kidney, swine kidney), or STE (swine testicular epitheloid); or general-purpose cell lines such as: Vero (African green monkey kidney cells), MDCK (Madin Darby canine kidney), or PT cells (ovine epithelial kidney cells). Preferred host cells are SK-6 or PK-15 cells. Specifically the pestivirus of the invention could be easily propagated on SK-6 or PK-15 cells to high titers (>10⁷) without the need for adaptation. This makes the inventive pestivirus highly advantageous for efficient preparing of vaccine compositions as well as for use as a viral vector.

At certain points in the viral replication cycle, such a host cells will contain a pestivirus of the invention. Therefore in a further aspect, the invention relates to a host cell comprising a pestivirus according to the invention, or as obtainable by a method of the invention.

For propagation, a host cell culture is infected with a polynucleotide, a vector, or a chimeric pestivirus as described herein, the host cell culture is incubated for virus propagation under appropriate conditions, the host cell culture is harvested completely or partially, and the virus is isolated from the cell culture or its supernatant. Optionally a pharmaceutically acceptable carrier is added to the virus or cell culture.

The present invention also refers to following items:

1. An isolated polynucleotide comprising a nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 2 or a sequence with at least 60%, specifically at least 70% identity thereto.

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-232. The polynucleotide of item 1 which is an infectious polynucleotide.

3. The polynucleotide according to item 1 or 2, wherein the polynucleotide is present in a cell.

4. The polynucleotide according to any one of items 1 to 3, wherein an RNA polymerase promoter is operably linked to the polynucleotide.

5. The polynucleotide according to any one of items 1 to 4, wherein the polynucleotide further comprises an exogenous polynucleotide.

6. The polynucleotide according to any one of items 1 to 4, wherein the polynucleotide is present in a vector.

7. A cDNA polynucleotide of SEQ ID NO: 1.

8. A cDNA polynucleotide having at least 65%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95% homology to SEQ ID NO: 1.

9. An infectious polynucleotide comprising a sequence selected from the group of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29 or any combinations thereof or a sequence with at least 95% identity thereto.

10. A composition comprising a porcine pestivirus having a nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 2 or a sequence with at least 60%, specifically at least 70% identity thereto.

11. A composition comprising a porcine pestivirus comprising an amino acid sequence of SEQ ID NO: 3 or a sequence having at least 60% identity thereto.

12. A composition comprising a porcine pestivirus comprising one or more amino acid sequences selected from the group consisting of SEQ ID NO: 4 (Npro), SEQ ID NO: 5 (Core), SEQ ID NO: 6 (Erns), SEQ ID NO: 7 (E1), SEQ ID NO: 8 (E2), SEQ ID NO: 9 (P7), SEQ ID NO: 10 (NS2), SEQ ID NO: 11 (NS3), SEQ ID NO: 12 (NS4A), SEQ ID NO: 13 (NS4B), SEQ ID NO: 14 (NS5A) and SEQ ID NO: 15 (NS5B).

13. The composition according to any one of items 10 to 12, wherein the porcine pestivirus is inactivated or attenuated.

14. The composition of item 13, wherein said pestivirus is a chemically inactivated virus which is specifically inactivated by treatment with an inactivating agent selected from the group consisting of binary ethyleneimine, ethyleneimine, acetylethyleneimine, beta-ethyleneimine, beta-propiolactone, glutaraldehyde, ozone, and formaldehyde.

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15. The composition of item 13, wherein the pestivirus is a physically inactivated pestivirus which is inactivated by treatment with UV radiation, X-ray radiation, gamma-radiation, freeze-thawing, and/or heating.

16. The composition of item 13, wherein the pestivirus is an attenuated by modifying the Npro, Erns or N2-3 genes.

17. The composition according to any one of items 10 to 16, comprising the pestivirus in freeze-dried form.

18. The composition according to any one of items 10 to 17, comprising a TCID5O at least about 1x10⁴.

19. Pharmaceutical composition comprising a composition according to any one of items 10 to 18.

20. Porcine pestivirus vector comprising nucleotide sequence SEQ ID NO: 2, or a sequence having at least 60%, specifically at least 70% identity thereto and a sequence encoding a heterologous sequence.

21. The vector of item 20, wherein the heterologous sequence is selected from a virus selected from the group consisting of APPV, NRPV, porcine circovirus 2 (PCV2), Bungowannah virus, bovine viral diarrhea virus (BVDV) specifically BVDV-1, BVDV-2, classical swine fever virus (CSFV), RaPV and border disease virus, specifically said heterologous sequence encodes a surface antigen from said viruses.

22. The vector according to any one of items 20 or 21, wherein heterologous sequence is inserted at the 5'or 3'end of Npro.

23. The vector according to any one of items 25 or 27, wherein the heterologous sequence encodes a fusion peptide with the Npro, the E2 or the E1 protein of the pestivirus.

24. Chimeric pestivirus having comprising a nucleotide sequence having at least 60%, specifically at least 70% identity to SEQ ID NO: 1 or SEQ ID NO: 2, and a foreign polypeptide.

25. Vaccine for animals comprising a polynucleotide according to any one of items 1 to 9, or a composition according to any one of items 10 to 18, or a vector according to any one of items 20 to 23, or a chimeric pestivirus according to item 24.

26. Kit for inducing an immune response against porcine pestivirus infection in a pig, said kit comprising a composition according to any one of items 10 to 18 and instructions for administering said composition to said pig.

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27. A method for protecting a piglet against a disease associated with pestivirus, wherein the method comprises administering to a pregnant sow, a boar, a post weaner, a gilt, or to a sow or gilt prior to breeding, the composition of any one of items 10 to 18, in an amount sufficient to protect the piglet.

28. The method according to item 27, wherein the disease is congenital tremor, specifically congenital tremor A-ll.

29. The method according to items 27 or 28, wherein the composition is parenterally administered, specifically intramuscularly, subcutaneously, intradermally, or intravenously using a needle and syringe, or a needleless injection device; or via mucosal administration, specifically nasally or orally.

30. Method for detecting pestivirus, wherein a sample is tested with RT PCR using at least one of the primers selected from SEQ ID NO: 32 and SEQ ID NO: 33.

31. Diagnostic assay for detecting pestivirus, comprising at least one of the primers selected from SEQ ID NO: 32 and SEQ ID NO: 33.

32. Method for detecting pestivirus antigen having an amino acid sequence of SEQ ID NO: 3 or an amino acid sequence of at least 60% identity in a biological sample, said method comprising:

contacting a biological sample with monoclonal antibody 6A5 antibody, said monoclonal antibody specifically binding to an antigen of said pestivirus if present in said sample; and detecting antibody binding to said antigen in said sample.

33. Method for preparing a vaccine according to item 32, comprising the sequential steps of

a) Infecting a host cell culture with a polynucleotide according to any one of items 1 to 9, a vector according to any one of items 20 to 23, or a chimeric pestivirus according to item 24,

b) Incubating said host cell culture for virus propagation,

c) Harvesting the host cell culture, and optionally

d) Isolating the virus from the culture and

e) Admixing to the culture with a pharmaceutically acceptable carrier.

34. Use of a polynucleotide according to any one of items 1 to 9, or a composition according to any one of items 10 to 18, or a vector according to any one of items 20 to 23, or a chimeric pestivirus according to item 24 or any combination thereof, for preparing a vaccine for animals.

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35. A polynucleotide according to any one of items 1 to 8, or a composition according to any one of items 10 to 18, or a vector according to any one of items 20 to 23, or a chimeric pestivirus according to item 24 or any combination thereof, for use in a vaccine for animals.

36. Method for controlling an infection with a pestivirus in animals, wherein the vaccine according to item 25 is combined with a diagnostic kit according to item 26.

The present invention is further illustrated by the following examples without being limited thereto.

EXAMPLES

Example 1:

An Austrian piglet-producing farm recorded an outbreak of severe repetitive myoclonia in newborn piglets. Histological examination of the central nervous system (CNS) of affected piglets revealed a hypomyelination of the white substance in cerebellum and spinal cord. During the search for Atypical porcine pestivirus (APPV) genomes in the affected piglets, a previously unknown pestivirus strain - provisionally termed “Linda virus” - was discovered. This virus was isolated from serum samples and could be readily propagated in cultured porcine cells. A full genomic sequence was determined using primer walking together with Sanger sequencing and RACEPCRs. Pairwise alignment of Linda sequences with other known pestivirus species and unassigned strains revealed a nucleotide identity of less than 68% and an amino acid identity of less than 70% to its closest relative, Bungowannah virus. Within a broad panel of more than hundred monoclonal antibodies raised against the pestivirus species BVDV-1, BVDV-2, CSFV and Bungowannah virus, one E2 specific antibody reactive against Linda virus was identified. Using the E2 specific antibody, the presence of Linda in the CNS of affected piglets at the site of lesions was confirmed. In conclusion, a putative novel pestivirus species is described herein which causes congenital tremor in European domesticated swine clearly distinct from the recently discovered APPVs.

Here, the discovery and molecular characterization of a novel porcine pestiviruses strain is reported that is provisionally termed “Linda” and is unrelated to APPV. The virus was found in an Austrian pig farm reporting major losses due to the “shaking piglet” syndrome. The course of disease was similar to recent APPV

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-27outbreaks in Austria (Schwarz et al., 2016, above) but clinical signs and pathological lesions were more pronounced. Histopathological examinations showed that the severe clinical signs were linked to an apparent hypomyelination in the cerebellum and spinal cord. Linda pestivirus was isolated from sera and tissue samples of affected piglets and propagated to high titers on porcine cell lines. The infected tissue cultures were used to identify monoclonal antibodies (mAb) reactive against Linda virus. Using these mAbs, the protein expression of Linda virus was detected by immunohistochemistry at the site of lesions in the central nervous system (CNS). A full genomic sequence of strain Linda was determined by RT-PCR, substantiating the affiliation of Lind virus to the genus pestivirus. Phylogenetic analysis showed that Linda virus is most closely related to Bungowannah virus. However, the divergence observed between Linda and Bungowannah virus was greater than between the approved pestiviral species BDV, BVDV and CSFV. Hence, strain Linda is proposed as a novel species within the genus Pestivirus.

2. Material and Methods

2.1. Sample collection

All animal use protocols employed in this study are approved by the institutional ethics and animal welfare committee and the national authority according to No endangered or protected species were involved in the study. Solely privately owned land was used for sample collection and accessed only after permission from the owner. In 2015 samples were obtained by the contracted veterinarian from a small scale Austrian piglet-producing farm, which reported major piglet losses due CT. Farm L had not used any vaccines against CSFV or other pestiviruses according to the Austrian legislation. Veterinarians of the University Clinic for Swine in Vienna visited farm L and collected further samples for diagnostic evaluation.

2.2. Description of the farm L

Farm L is a piglet production site located in Styria in the southern part of Austria. In total 25 Large-white x Landrace crossbred sows are managed in continuous farrowing cycles. CT affected litters solely occurred in gilts and were not observed in following litters. The gilts were obtained from a gilt producer, who was not reporting problems with CT. All gilts were vaccinated against parvovirosis and erysipelas (Parvoruvac®, Merial SAS, Lyon, France) and treated alternately with fenbendazole (Panacur4%, Intervet, Vienna) and ivermectine (Ivomec, Merial SAS, Lyon, France) to

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-28prevent introduction of sarcoptic mange and round worms. This herd was free of PRRSV before and after occurrence of CT.

2.3. Pathology

A complete necropsy was performed on eight piglets of farm L originating from two different litters. The findings from six clinically affected piglets and two healthy littermates without symptoms were compared. The piglets were euthanized; a gross pathological examination was performed and samples were taken. For histological examination brain, spinal cord, and organ samples of all piglets and healthy control animals from a farm without CT problems were fixed in 10% neutral buffered formalin. Formalin fixed brains were cut into coronary sections of 2-3 mm thickness and embedded in paraffin wax. Organ samples and coronary and longitudinal sections of cervical, thoracic and lumbar spinal cord were cut and embedded in paraffin wax, too. Of all embedded organs 1.5 pm thick sections were cut and stained with hematoxylin and eosin (HE). Furthermore, brain and spinal cord samples were stained with a combination of luxol fast blue and HE (LFB-HE) to determine the extent of myelination. Immunohistochemical investigations using a primary anti pan-pestivirus E2 antibody (mAb 6A5, dilution 1:1000) for detection of Linda were performed automatically on an autostainer (Lab Vision AS 360, Thermo Fisher Scientific, Waltham, USA). Briefly, 2 pm paraffin-embedded sections of the piglets’ brains and spinal cords were placed on coated slides and dried to enhance tissue adherence. Antigen retrieval was performed on deparaffinized and rehydrated sections by heating in citrate buffer (pH 6). Endogenous peroxidase activity was blocked by incubation in H2O2. After application of the primary antibody a polymer detection system (UltraVision LP Large Volume Detection System; Thermo Fisher Scientific, Waltham, USA), consisting of a universal secondary antibody formulation conjugated to an enzyme-labeled polymer was used. The polymer complex was then visualized with an appropriate substrate/chromogen (diaminobenzidine [DAB]; Labvision/Thermo Fisher Scientific, Waltham, USA). Subsequently, all sections were counterstained with hematoxylin, dehydrated and mounted.

2.4. Detection of APPV genomes

Total RNA was extracted from field serum or tissue samples using the QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was eluted in 60 pl RNase free distilled water and directly used for RT-PCR or stored at -80 °C for subsequent analysis. RT-PCR was carried out using

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-29the OneTaq One-Step RT-PCR Kit (NEB, Ipswich, USA) or the One Step RT-PCR Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. A panpestivirus RT-PCR protocol was developed to detect atypical pestiviruses using the oligonucleotides PPF (5’-GTKATHCAATACCCTGARGC-3’, SEQ ID NO: 32) and PPR (5’-GGRTTCCAGGARTACATCA-3’, SEQ ID NO: 33), an annealing temperature of 55 °C, and an elongation time of 1 min.

2.5. Virus isolation and growth

For virus isolation, 50 μΙ serum or 50 μΙ of homogenized tissue samples of diseased piglets from the affected farm L were used to inoculate 5 x 106 SK-6 cells on a six-well plate. After three days, the cell culture supernatant was harvested, cleared by centrifugation and passaged on fresh SK-6 cells. All cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum (FCS Gold Plus, Bio&Sell, Feucht, Germany) and maintained at 37°C and 5% CO2. Virus infections and passages were analyzed by RT-PCR and immunofluorescence.

2.6. Monoclonal antibodies against strain Linda

Monoclonal antibodies were generated against most proteins of CSFV and BVDV in previous studies. Furthermore, antibodies were raised against E2 and NS3 of Bungowannah virus (unpublished data). Briefly, BALB/c mice were immunized with recombinant proteins until seroconversion was observed. Spleen cells were prepared and fused with sp2/0-AG14 myeloma cells to generate monoclonal antibody producing hybridomas. The resulting mAbs were evaluated using ELISA, mmunoblot and immunofluorescence assays as needed. Each of these fusion experiments yielded up to 100 different reactive monoclonal antibodies generating an extensive collection of antibodies against the pestiviral proteins. Several E2-specific and NS3-specific panels of cross-reactive antibodies were screened by an indirect immunofluorescent assay using Linda virus infected cell cultures.

2.7. Determination of the full genomic sequence

Several primer pairs (available upon request) that were hybridizing with highly conserved regions in different pestivirus species (BVDV, BDV, CSFV, Bungowannah, and APPV) were designed according to published sequences available in GenBank. To determine the sequence of the ultimate 5’- and 3’-termini, RACE-PCRs were performed. Total RNA purified from virus infected cell cultures was ligated to two different adapter oligonucleotides using T4 RNA ligase I (NEB, Ipswich, USA). A nonphosphorylated standard oligonucleotide (AD1, 5’-GGCCACGCGTCGACTAGTAC-3’

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-30OH, SEQ ID NO: 34) was used for 5’-RACE and a phosphorylated oligonucleotide blocked at the 3’ end by an amine group for 3’-RACE (AD2, PO3-5’GGCCACGCGTCGACTAGTAC-3’-AmC3, SEQ ID NO: 35). For cDNA generation and subsequent PCR amplification, primer hybridizing with Linda virus specific sequences and adapter primer (AD1 or ADIrev) were applied together with reverse transcriptase (Superscript II, Thermo Fisher Scientific) and high fidelity Taq-Polymerase (One Taq, NEB). A second PCR was employed using the adapter oligonucleotide (AD1 or ADIrev) together with a nested Linda sequence specific primer to amplify the desired 5’- and 3’-termini. PCR amplicons were subjected to gel electrophoresis, purified by the peqGOLD Gel Extraction Kit (Peqlab, Erlangen, Germany) and sequenced by a commercial provider (Eurofins Genomics, Ebersberg, Germany). In addition, all Linda cDNA fragments were sub-cloned in the pGEM-T easy vector (Promega. Madison, USA) and re-sequenced from the plasmid to obtain high quality sequencing results. The sequence of the pestivirus strain Linda was submitted to GenBank and is listed below as SEQ ID NO: 1. First analyses were carried out using NCBI’s basic local alignment search tool for nucleotides (BLASTn) and proteins (BLASTp). Phylogenetic pairwise comparison and identity calculations were carried out with CLC Main Workbench 7.6 (CLCBIO, Aarhus, Denmark). Alignments and phylogenetic trees were generated with the software CLC Sequence Viewer 7.6 (CLCBIO, Aarhus, Denmark) with bootstrap values based on 1,000 replicates. For construction of the phylogenetic trees, sequences of other pestivirus species deposited in GenBank were used as indicated.

3. Results

3.1. Description of the clinical signs in the affected farm L

In July 2015, first signs of CT were observed in newborn piglets of sows that had farrowed for the first time: between 20% and 100% of the newborn piglets from these litters showed a horizontal shaking involving the whole body. Many newborn piglets were incapable of sucking milk and died before weaning. The shaking vanished in single affected piglets over time, yielding unsuspicious post-weaners. The outbreak of CT ended in September of 2015 with the last litter of newly farrowing gilts.

3.2. Pathology

Piglets from two CT affected litters showed no or only mild lesions on gross examination. Excoriations of the legs, alveolar lung edema and emphysema were found. Some of the CT affected piglets showed scattered petechiae in the renal cortex

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-31and in the spinal cord, which were not related to euthanasia. The spinal cord of CT affected piglets appeared slightly hypotrophic. Accentuated vacuoles were present in the white matter of the cerebellum of all clinically affected animals (n=6/6), while fewer vacuoles were found in the unaffected littermates in HE-LFB-staining (Fig. 1A, B). Hypomyelination and hypoplasia were evident in the white matter of the cerebellum and spinal cord of affected piglets and unaffected littermates compared to the healthy control (Fig. 1).

3.3. Detection of Linda virus

A pan-pestivirus RT-PCR targeting a well conserved NS5B region was developed to detect atypical pestiviruses using a novel set of primers. This assay was successfully evaluated using cultures of BVDV-1, BVDV-2, CSFV, BDV, Bungowannah virus and recently isolated APPV strains (Schwarz et al., 2016). Using this RT-PCR assay and clinical samples of CT affected piglets of farm L, an amplicon of appropriate length was obtained. The 815 bp amplicon was sequenced using the PCR primer yielding an unknown sequence with non-interrupted open reading frame. An initial BLASTn search resulted in “no significant similarity found”, but the translated amino acid sequence of 270 amino acid aligned with different pestiviruses. Alignments covered Bungowannah virus (YP_008992092.1, identity 84%, E-value 1e-154), CSFV (NP_777506.1, identity 78%, E-value 2e-153), BDV (NP_777545.1, identity 77%, Evalue 9e-151), and BVDV-1 (1S4F_A, identity 75%, E-value 6e-150). The viral RNA sequence was found in clinical samples of all piglets from CT litters examined from farm L (serum, tonsils, lung, liver, spleen and CNS material), whether CT affected or not. In contrast, serum samples of mother sows of farm L were negatively tested for the presence of nucleic acid of strain Linda. 3.4. Genomic sequence and phylogenetic genome analysis

The full genome of Linda was determined using the standard primer walking RTPCR approach together with RACE-PCR to identify the ultimate 5’- and 3’-termini. A total of 12,614 nucleotides (nt) were determined for Linda virus representing 381 nt of the 5’-NTR, 461 nt of the 3’-NTR and 11,772 nt of the coding region (ORF). Nucleotide identity between Linda and its closest relative, Bungowannah virus, was below 68.0% with a sequence alignment coverage of only 88%. Only short stretches of highly similar nucleotide alignments within the conserved genes with other pestiviruses covering less than 42% of their genome were obtained. Consequently, the identities between Linda and BVDV-1, BVDV-2, BDV, APPV or CSFV were below 60%. As apparent, the

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-32distance to Bungowannah virus as well as to the classical pestivirus species is considerable. A phylogenetic genome analysis of Linda virus, atypical pestivirus strains and the pestiviral type strains is shown in figure 2.

3.5. ORF-Analysis

The ORF of Linda contains 3,924 codons; more codons than the ORF of any other known pestivirus genome, except for BVDV strains with foreign gene insertions. Comparison of the amino acid sequence of Linda with other pestiviruses available in GenBank yields an amino acid identity of 69% with Bungowannah virus (YP_008992092.1), 53% with BVDV-3 (BAO04453.1), 53% with BDV (AHM88396.1), 53% with CSFV (AGE89843.1), 52% with BVDV-2 (CDH30717.1), and 52% with BVDV-1 (AEW46241.1) with expected values of 0.0 each. The phylogenetic analysis of pestiviral polyproteins is shown in figure 3. All hypothetical polyprotein processing products of Linda virus match best with the mature proteins of Bungowannah virus. The identity score to Bungowannah virus were determined with 63% for Npro (AA1182), 83% for Core (AA183-283), 74% for Erns (AA284-504), 67% for E1 (AA505-702), 53% for E2 (AA703-1077), 59% for P7 (AA1078-1152), 63% for NS2 (AA1153-1608), 85% for NS3 (AA1609-2291), 81% for NS4A (AA2292-2354), 78% for NS4B (AA23552701), 53% for NS5A (AA2702-3205), and 73% for NS5B (AA3206-3923). Signal peptide cleavage sites were annotated in analogy to experimental determined protein borders of classical pestiviruses and confirmed using in silico prediction. In difference to other pestiviruses, the NS3 mediated cleavage between the nonstructural proteins NS4A and NS4B takes place at a leucine/serine site in Linda virus, just like in Bungowannah virus. The specific intramolecular leucine/alanine cleavage site (L1834/A1835) within the NS3 separating protease and helicase domains is present in Linda virus.

3.6. Analysis of Linda virus E2

The pestiviral envelope protein E2 forms homodimers and E1-E2 heterodimers on the virus surface that mediate attachment and entry into host cells via receptor mediated endocytosis. Convalescent hosts develop an antibody response against the E2 protein that is crucial for virus neutralization. The E2 protein is responsible for the pestivirus species specific host tropism and exhibits the greatest amount of diversity among all pestiviral proteins. Linda virus E2 was 53% identical to the Bungowannah virus E2 (Fig. 4). All E2 proteins, except for the shorter Rat pestivirus and APPV E2 with only 241-244 amino acids, show a comparable length (373-378 AA) and shared a

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-33three domain structure. APPV and Bat pestivirus E2 contains 8 cysteines, CSFV E2 15 cysteines, Linda virus E2 16 cysteines, BVDV-1, BVDV-2, BVDV-3, Sheep, Reindeer, Giraffe, Rat pestivirus, and BDV E2 17 cysteines, Pronghorn pestivirus E2 18 cysteines and Bungowannah virus 19 cysteines. The up to eight intramolecular disulfide bonds form the structural units of E2 protein domains and free cysteines mediate intermolecular dimerization of E2-E2 homodimers or E1-E2 heterodimers. The typical cysteine positions are conserved in Linda virus and in analogy to BVDV, the cysteine in the E2 of Linda virus at position 296 is mediating heterodimer formation. Nlinked glycosylation (NLG), the addition of oligosaccharides to asparagine residues, requires recognition of the consensus sequence motive Asn-X-Ser/Thr. Pestiviral E2 contains three NLG sites in case of Pronghorn pestivirus, four NLG sites in case of BVDV-1, BVDV-2, Rat pestivirus, Giraffe pestivirus and Bungowannah virus, five NLG sites in BDV, APPV and Sheep pestivirus but up to six NLG sites in case of CSFV, BVDV-3, Reindeer pestivirus and Bat pestivirus. The heavy glycosylation is causing an increase of the molecular mass by glycan attachment and a masking of immunogenic protein surfaces. In contrast to all known pestiviral species, the sequence of Linda pestivirus includes only two potential NLG sites. Linda pestivirus E2 exhibits sequence similarities with the E2 molecules of the classical pestiviruses but shows distinct features.

3.6. Isolation and propagation of strain Linda

The availability of the RT-PCR assay allowed for detection of Linda infection of cultured cells. After initial inoculation of SK-6 cells with serum of a CT affected piglet and passage of cell culture supernatant, the successful isolation of Linda virus was shown by RT-PCR. The infection of SK-6 or PK-15 cells with Linda did not lead to an apparent cytopathic effect. Using established serological reagents and immunofluorescence, the presence of Linda antigen in SK-6, PK-15 and MDBK cells after infection was further demonstrated. Considerably high infectious titers of Linda were measured in the supernatant of infected porcine cell cultures (>107 TCID50 per ml, Fig. 5). In addition, a focus size assay employing porcine and bovine cell lines revealed about 10-fold larger antigen positive foci in SK-6 cells than in MDBK cells (Fig. 5B).

3.7. Serological reagents against strain Linda

Panels of immunofluorescence positive pestivirus specific mAbs, which were established in earlier studies, were screened for reactivity against Linda virus infected

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-34cell cultures. A strong reactivity against Linda infected cells was seen using the E2 specific antibody 6A5, generated against BVDV E2 (Fig. 6). The immunofluorescence of this antibody yielded a cytoplasmic signal with a dominant staining of membranes of the endoplasmic reticulum. This staining pattern has also been documented for the homologous proteins of other pestiviruses.

4. Discussion

In the course of investigating typical cases of CT for the presence of APPV, piglet producing farm L stood out because APPVs were not detected using a TaqMan probe based RT-PCR assay (Schwarz et al., 2016). This was surprising as the clinical observations were apparent and the lesions in the spinal cord and cerebellum of infected animals were pronounced.

A novel pan-pestivirus RT-PCR assay was designed to ensure the detection of APPV, BDV, BVDV-1, and BVDV-2, described earlier. Sequence analysis of the amplicons of six CT-affected piglets from farm L revealed a sequence of a so far unknown pestivirus. Further analyses of the assembled genome allowed an unambiguous assignment of Linda virus within the genus pestivirus, both with regard to the presence of pestivirus specific genes (Npro and Erns) as well as sequence homology to other pestiviruses in conserved genomic regions (NS3 and NS5B). The overall nucleotide identity between Linda and the closest related known pestivirus (Bungowannah virus) is below 68.0% suggesting that Linda virus represents a novel pestivirus species. The finding that Linda pestivirus very likely shares a common ancestor with Bungowannah virus is exciting. After its description about 10 years ago, it was intensively searched for Bungowannah virus all over the world but the virus was never detected outside Australia. Another feature of Linda pestivirus was remarkable and clearly distinct from APPV. APPV hardly infects cultured cells at all and isolation is challenging. Linda pestivirus could be easily propagated on SK-6 or PK-15 cells to high titers (>107) without the need for adaptation, similar to what has been reported for Bungowannah virus and CSFV. Worth mentioning is the fact that even though MDBK cell were permissive for Linda pestivirus, its growth was remarkable reduced compared to porcine cell lines. This suggests that Linda pestivirus is a genuine porcine pathogen.

According to the ICTV, the classification of pestiviruses is mainly based on host range, sequence homology and disease. The natural host of CSFV is pigs, the natural host of BDV is sheep, the natural host of BVDVs is cattle, and several atypical pestivirus strains found an ecological niche in different wildlife species. However, most

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-35pestivirus species are able to adapt on novel cloven hooved host species and show a broad host range after laboratory infections. In addition to the approved species, three groups of atypical pestiviruses have been described and categorized with respect to the natural hosts. Group 1 comprises all pestiviruses of bovine origin. Group 2 includes the pestiviruses of non-bovine and non-ovine origin, covering wildlife pathogens like the Pronghorn virus and also porcine pathogens like Bungowannah virus. Group 3 comprises the sheep isolates also referred to as the Tunisian pestiviruses. The discovery of Bungowannah virus, APPV and the description of Linda demands the establishment of a group 4 as the “porcine pestivirus group”. Regarding these categories, the inclusion of established species seems logical.

Species affiliation or demarcation based on the genetic relationship between different strains depends on the definition of type strains. Type strains exist for the classical pestiviruses (BVDV-1, strain NADL; BVDV-2, strain 890; BDV, strain X818; CSFV, strain A187) but were missing for the tentative species of atypical pestiviruses. The nucleotide sequence divergence between the complete genomes of established pestiviral species and the additional tentative species (Giraffe pestivirus, Pronghorn virus, BVDV-3, Sheep pestivirus, Rat pestivirus, Bungowannah virus, and APPV) exceeds 25%, thereby providing a robust minimal threshold (25%) for the affiliation or demarcation of novel strains. In a practical approach, a total of nine pestivirus species (BVDV-1, BVDV-2, BVDV-3, Giraffe pestivirus, CSFV, BDV, Sheep pestivirus, Antelope pestivirus and Bungowannah pestivirus) have been proposed before APPV was discovered. As a consequence of sequence variance, there is a pronounced antigenic variance between the different pestivirus species. Since sera of convalescent animals show a much higher neutralization titer against pestiviral strains from the homologous species than against pestiviral strains from heterologous species, the species relation can also be grouped by serotypes taken the cross-reactivity of immune sera into account. In the case of Linda virus, sera of defined convalescent animals could not be obtained from the farm L and hence, cross-species neutralization tests could not be performed. Controlled laboratory infection studies would be needed to answer the question if immune sera from Linda infected animals were able to neutralize other pestivirus species. It is planned to investigate, if the available ELISA systems for CSFV and BVDV diagnostics show interference with Linda virus infections. A collection of murine monoclonal antibodies were tested against different pestiviral proteins of different species -- except of BDV -- and found that most established

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-36reagents were not reactive against Linda. Even pan-pestivirus specific IgGs, like mAb

8.12.7. which is reactive against CSFV, BVDV-1, BVDV-2, and BDV, failed to detect Linda infected cells (data not shown). Interestingly, none of the Bungowannah specific mAbs cross reacted with Linda virus. These analyses suggested that Linda virus exhibit a considerable antigenic difference to the established pestiviral species and to Bungowannah virus.

Linda virus was detected retrospectively in a single farm that was tested virus free several months after the clinical signs had ceased. In contrast to the mostly mild form of CT in APPV affected piglets that improve from central nervous defects with age, the clinical signs associated with Linda virus were severe in most piglets and frequently led to death. Strong evidence that Linda virus is the causative pathogen of the CNS damage and the hypomyelination comes from the clear detection of Linda virus E2 in the lesions of the periaxonal space. Currently, there is no link to other forms of disease in pigs so that experimental infections are required to assess pathogenicity and virulence of the new virus. The feasibility to grow Linda virus allows to challenge Koch’s postulates and define pathogenesis in controlled animal trials. Because the source of Linda virus introduction into the herd can only be speculation, further work is necessary on the prevalence and epidemiology of Linda virus in Austria.

Example 2:

Animal trial Linda virus

An animal trial was set up to investigate Linda virus pathogenesis and shedding. 21 post-weaning piglets (Sus scrota domestica, 12 weeks old) were housed in a biological safety unit (BSL2) in three different groups. After one week, 5 animals were intra-nasally and 5 animals were intra-muscularly infected with 1 χ 10^Λ7 tissue infectious doses 50% (TCID50) of Linda virus. A group of 5 animals was mock infected and served as a separated control, while 3 sentinel animals were included in the infection groups at the day post infection. The health status of all animals was assessed daily and the body weight was measured. Viremia and virus shedding was assessed at day 0 (day of infection), 3, 5, 7, 14, 21, and 28 post infection analyzing serum samples, nasal and oral swaps, and fecal samples. The animal trail showed, that:

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1. Linda is of low pathogenicity for post-weaners (no obvious fever, no obvious growth retardation, slightly reduced weight gain)

2. Linda leads to fast and reliable sero-conversion (neutralizing antibodies detectable in 10 of 10 infected pigs -- 5 i.n. and 5 i.m - all SNT titers >1:256) even after natural infection routes (SNT titer > 1:100 in the infected sentinel animal)

3. Linda is a contagious pathogen for pigs (1 of 6 sentinels infected)

4. Linda is causing a short-lasting viremia (infectious virus only observed in

i.m. animals and in the sentinel, at a single test time point each, test scheme: d3, d7, d14, d21,d28)

5. Linda is secreted via oro-nasal fluids (virus detection via RT-PCR positive in three infected animals at day 7 and/or day 14)

Claims (10)

1. An isolated polynucleotide comprising a nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 2 or a sequence with at least 60%, specifically at least 70% identity thereto.

2. The polynucleotide of claim 1 which is an infectious polynucleotide.

3. The polynucleotide according to claims 1 or 2, wherein the polynucleotide is present in a cell.

4. The polynucleotide according to any one of claims 1 to 3, wherein an RNA polymerase promoter is operably linked to the polynucleotide.

5 thereof, for preparing a vaccine for animals.

35. A polynucleotide according to any one of claims 1 to 8, or a composition according to any one of claims 10 to 18, or a vector according to any one of claims 20 to 23, or a chimeric pestivirus according to claim 24 or any combination thereof, for use in a vaccine for animals.

5. The polynucleotide according to any one of claims 1 to 4, wherein the polynucleotide further comprises an exogenous polynucleotide.

6. The polynucleotide according to any one of claims 1 to 5, wherein the polynucleotide is present in a vector.

7. A cDNA polynucleotide of SEQ ID NO: 1.

8. A cDNA polynucleotide having at least 65%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95% homology to SEQ ID NO: 1.

9. An infectious polynucleotide comprising a sequence selected from the group of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29 or any combinations thereof or a sequence with at least 95% identity thereto.

10. A composition comprising a porcine pestivirus having a nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 2 or a sequence with at least 60%, specifically at least 70% identity thereto.

11. A composition comprising a porcine pestivirus comprising an amino acid sequence of SEQ ID NO: 3 or a sequence having at least 60% identity thereto.

12. A composition comprising a porcine pestivirus comprising one or more amino acid sequences selected from the group consisting of SEQ ID NO: 4 (Npro), SEQ ID NO: 5 (Core), SEQ ID NO: 6 (Erns), SEQ ID NO: 7 (E1), SEQ ID NO: 8 (E2), SEQ ID NO: 9 (P7), SEQ ID NO: 10 (NS2), SEQ ID NO: 11 (NS3), SEQ ID NO: 12 (NS4A), SEQ ID NO: 13 (NS4B), SEQ ID NO: 14 (NS5A) and SEQ ID NO: 15 (NS5B).

13. The composition according to any one of claims 10 to 12, wherein the porcine pestivirus is inactivated or attenuated.

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14. The composition of claim 13, wherein said pestivirus is a chemically inactivated virus which is specifically inactivated by treatment with an inactivating agent selected from the group consisting of binary ethyleneimine, ethyleneimine, acetylethyleneimine, beta-ethyleneimine, beta-propiolactone, glutaraldehyde, ozone, and formaldehyde.

15. The composition of claim 13, wherein the pestivirus is a physically inactivated pestivirus which is inactivated by treatment with UV radiation, X-ray radiation, gamma-radiation, freeze-thawing, and/or heating.

16. The composition of claim 13, wherein the pestivirus is an attenuated by modifying the Npro, Erns or N2-3 genes.

17. The composition according to any one of claims 10 to 16, comprising the pestivirus in freeze-dried form.

18. The composition according to any one of claims 10 to 17, comprising a TCID₅₀ of at least about 10⁴..

19. Pharmaceutical composition comprising a composition according to any one of claims 10 to 18.

20. Porcine pestivirus vector comprising nucleotide sequence SEQ ID NO: 2, or a sequence having at least 60%, specifically at least 70% identity thereto and a sequence encoding a heterologous sequence.

21. The vector of claim 20, wherein the heterologous sequence is selected from a virus selected from the group consisting of APPV, NRPV, porcine circovirus 2 (PCV2), Bungowannah virus, bovine viral diarrhea virus (BVDV) specifically BVDV-1, BVDV-2, classical swine fever virus (CSFV), RaPV and border disease virus, specifically said heterologous sequence encodes a surface antigen from said viruses.

22. The vector according to any one of claims 20 or 21, wherein heterologous sequence is inserted at the 5'or 3'end of Npro.

23. The vector according to any one of claims 20 to 22, wherein the heterologous sequence encodes a fusion peptide with the Npro, the E2 or the E1 protein of the pestivirus.

24. Chimeric pestivirus having comprising a nucleotide sequence having at least 60%, specifically at least 70% identity to SEQ ID NO: 1 or SEQ ID NO: 2, and a foreign polypeptide.

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25. Vaccine for animals comprising a polynucleotide according to any one of claims 1 to 9, or a composition according to any one of claims 10 to 18, or a vector according to any one of claims 20 to 23, or a chimeric pestivirus according to claim 24.

26. Kit for inducing an immune response against porcine pestivirus infection in an animal, said kit comprising a composition according to any one of claims 10 to 18 and instructions for administering said composition to said animal.

27. A method for protecting a piglet against a disease associated with pestivirus, wherein the method comprises administering to a pregnant sow, a post weaner, a gilt, or to a sow or gilt prior to breeding, the composition of any one of claims 10 to 18, in an amount sufficient to protect the piglet.

28. The method according to claim 27, wherein the disease is congenital tremor, specifically congenital tremor A-ll.

29. The method according to claims 27 or 28, wherein the composition is parenterally administered, specifically intramuscularly, subcutaneously, intradermally, or intravenously using a needle and syringe, or a needleless injection device; or via mucosal administration, specifically nasally or orally.

30. Method for detecting pestivirus, wherein a sample is tested with RT PCR using at least one of the primers selected from SEQ ID NO: 32 and SEQ ID NO: 33.

31. Diagnostic assay for detecting pestivirus, comprising at least one of the primers selected from SEQ ID NO: 32 and SEQ ID NO: 33.

32. Method for detecting pestivirus antigen having an amino acid sequence of SEQ ID NO: 3 or an amino acid sequence of at least 60% identity in a biological sample, said method comprising:

contacting a biological sample with monoclonal antibody 6A5 antibody, said monoclonal antibody specifically binding to an antigen of said pestivirus if present in said sample; and detecting antibody binding to said antigen in said sample.

33. Method for preparing a vaccine according to claim 32, comprising the sequential steps of

a) Infecting a host cell culture with a polynucleotide according to any one of claims 1 to 9, a vector according to any one of claims 20 to 23, or a chimeric pestivirus according to claim 24,

b) Incubating said host cell culture for virus propagation,

c) Harvesting the host cell culture, and optionally

d) Isolating the virus from the culture and

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e) Admixing to the culture with a pharmaceutically acceptable carrier.

34. Use of a polynucleotide according to any one of claims 1 to 9, or a composition according to any one of claims 10 to 18, or a vector according to any one of claims 20 to 23, or a chimeric pestivirus according to claim 24 or any combination

10 36. Method for controlling an infection with a pestivirus in animals, wherein the vaccine according to claim 25 is combined with a diagnostic kit according to claim 26.